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Belgium will this week attempt to return to politics as normal after a week that overturned settled expectations and saw the choice of a European commissioner take precedence over determining who would be the country’s next prime minister.

The decision of the Flemish Christian Democrat Party, CD&V, to insist on the nomination of Marianne Thyssen as the country’s European commissioner, and in doing so to surrender its claim to the prime ministership, constituted a break from what has become the natural order of Belgian politics.

Herman Van Rompuy, himself a former CD&V prime minister of Belgium – the post he forsook five years ago to become president of the European Council – when interviewed on Flemish television on Sunday admitted that he had seen nothing like it.

The Flemish Christian Democrats have supplied most of the post-1945 prime ministers and although the party is nowhere near as powerful as it once was, there was a general expectation that Kris Peeters, a former CD&V minister-president of Flanders, would head the federal government and so extend the lineage of prime ministers from the party that in the past 30 years has included Wilfried Martens, Jean-Luc Dehaene, Yves Leterme and Herman Van Rompuy.

Peeters shared that expectation. He admitted on Friday that he had been taking French lessons from 8am-11am each day. He had discussed becoming prime minister with Bart De Wever, the leader of the Flemish right-wing party N-VA, who had declared after the 25 May election that though his was by some distance the biggest party in Flanders, it would not supply the prime minister.

The negotiations to form a federal government involve three parties from the Flemish side – N-VA, CD&V and the Flemish liberal party, VLD – but just one party on the Walloon side – the liberal party Mouvement Réformateur. MR wanted Didier Reynders, the foreign minister, who was for several years the finance minister, to become European commissioner. CD&V’s insistence that the job should go to Thyssen meant that Peeters would not become prime minister. Peeters admitted that Wednesday night had been emotionally turbulent, but said the decision to forgo the prime ministership was a logical consequence of the party’s conviction that Thyssen was the right choice.

The parties negotiating over a government agreed that “the liberal family” would supply the prime minister. In practice, this means it will go to MR, either to Reynders, or, perhaps more likely, to Charles Michel, a son of Louis Michel, foreign minister in a Verhofstadt government and later a European commissioner. Belgium has not had a francophone liberal prime minister since May 1938, so the political world is faced with a result quite as strange as the appointment of Elio Di Rupo, a francophone socialist, as prime minister, in 2011 – the first prime minister from a francophone party since 1979.

The calculation that MR will have to make is what the political consequences might be of heading a government driven by N-VA. A francophone party could be put in difficulties, but MR’s calculation is likely to be that constitutional and institutional reforms have been made by the previous government. For the coming government – as Peeters himself said in a television interview on Sunday – the challenge is economic and social reform, including changes to pensions, tax, employment rights and social security entitlements. On these issues, MR will probably find it easier to find common cause with N-VA than would CD&V, which for all that it is aligned with the centre-right EPP in the European Parliament will effectively be the left-wing of the government that is in formation. Indeed, Peeters made an appeal in his television interview to the trade union arm of his party – the ACV – to back social and labour market reform. His decision not to seek the prime ministership is interpreted by some as a sign that he does not have the pre-eminence in the party that he once had – and perhaps a sign of the growing influence of Wouter Beke, the party chairman who led for CD&V in the negotiations on government formation.

In Belgium, the choice of European commissioner has taken precedence over the choice of prime minister for three reasons:

Firstly, a matter of poor timing: the choice of commissioner could not be delayed until the completion of the drawn-out negotiations over the federal government. It did not help that, because of the institutional reforms of the last few years, the European elections coincided not just with the federal government elections but also the regional government elections, whose formation was negotiated first (and whose formation, for instance, determined that the Walloon centre party would not join the federal coalition). Jean-Claude Juncker, the incoming president of the European Commission, insisted on an answer.

Secondly, CD&V, while it is convinced that it must be a party of government, has learnt a lesson from the incumbency of Yves Leterme that the prime ministership can be a burden.

Thirdly, no one dissented from the view that Thyssen is well qualified to be European commissioner. Bruno Tobback, leader of the Flemish socialists, described her as “the right woman in the right place”. An agreement on the commissioner was actually easier than agreement on the prime minister.

Belgium’s head of state, Philippe, king of the Belgians, last week gave an indefinite mandate to the two men co-ordinating negotiations on the formation of the government, Peeters and Charles Michel, to pursue their talks. In his television interview Peeters said that with the appointment of Thyssen out of the way, the negotiations would “return to the normal procedure”. He expressed the hope that the experience of the past week would mean that the negotiations would advance better “in the coming days and weeks”.

When those negotiations might actually be completed is not the only matter of uncertainty: there are plenty of people wondering how long a difficult coalition might hold together. Thyssen’s five years as European commissioner might be much longer than the term of office of the next Belgian prime minister.